From b6d848eff00fd87340ac6c5d39904cfb3390e742 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ren=C3=A9=20Meier?= <meier.rene@googlemail.com>
Date: Thu, 24 Oct 2024 12:11:31 +0200
Subject: [PATCH] More dependency updates and cleanups.

---
 MetFragLib/pom.xml                            |  4 ++--
 MetFragRest/pom.xml                           | 21 +++++++++-------
 .../metfragrest/MetFragRestController.java    |  2 +-
 .../metfragweb/controller/MetFragWebBean.java |  6 ++---
 .../src/main/webapp/WEB-INF/faces-config.xml  | 11 ++++-----
 MetFragWeb/src/main/webapp/WEB-INF/web.xml    |  9 ++++---
 .../src/main/webapp/comparespectrad3js.xhtml  | 12 +++++-----
 .../includes/candiateScoreDistribution.xhtml  | 15 ++++++------
 .../includes/candidateFiltersPrime.xhtml      | 13 +++++-----
 .../candidateFiltersScoresPrime.xhtml         | 13 +++++-----
 .../includes/candidateScoresPrime.xhtml       | 15 ++++++------
 .../includes/comparespectraD3JSInclude.xhtml  | 15 ++++++------
 .../main/webapp/includes/databasePrime.xhtml  | 15 ++++++------
 .../webapp/includes/dialogs/aboutDialog.xhtml | 13 +++++-----
 .../dialogs/downloadCandidatesDialog.xhtml    | 11 +++++----
 .../dialogs/downloadParametersDialog.xhtml    | 11 +++++----
 .../dialogs/downloadResultsDialog.xhtml       | 11 +++++----
 .../dialogs/expiredSessionDialog.xhtml        | 11 +++++----
 .../dialogs/feedbackButtonDialog.xhtml        | 11 +++++----
 .../includes/dialogs/feedbackDialog.xhtml     |  6 ++---
 .../dialogs/fragmentsViewDialog.xhtml         | 13 +++++-----
 .../processCandidatesProgressDialog.xhtml     | 11 +++++----
 .../retrieveCandidatesProgressDialog.xhtml    | 11 +++++----
 .../includes/dialogs/scoresViewDialog.xhtml   | 13 +++++-----
 .../includes/dialogs/spectrumViewDialog.xhtml | 11 +++++----
 .../includes/errorpages/viewExpired.xhtml     | 11 ++++++---
 .../src/main/webapp/includes/footer.xhtml     |  9 +++----
 .../webapp/includes/fragmentationPrime.xhtml  | 15 ++++++------
 .../src/main/webapp/includes/header.xhtml     |  9 +++----
 .../main/webapp/includes/landingPage.xhtml    | 15 ++++++------
 .../src/main/webapp/includes/main.xhtml       | 15 ++++++------
 .../main/webapp/includes/resultCluster.xhtml  | 15 ++++++------
 .../main/webapp/includes/resultTable.xhtml    | 15 ++++++------
 .../src/main/webapp/includes/statistics.xhtml | 15 ++++++------
 .../tooltips/databasePrimeTooltips.xhtml      | 11 +++++----
 .../tooltips/filterPrimeTooltips.xhtml        | 11 +++++----
 .../tooltips/fragmentationPrimeTooltips.xhtml | 11 +++++----
 .../tooltips/scorePrimeTooltips.xhtml         | 11 +++++----
 .../webapp/includes/uploadParameters.xhtml    | 15 ++++++------
 MetFragWeb/src/main/webapp/index.xhtml        | 11 +++++----
 MetFragWeb/src/main/webapp/landing.xhtml      | 11 +++++----
 .../src/main/webapp/resources/css/style.css   | 24 -------------------
 MetFragWeb/src/main/webapp/upload.xhtml       | 11 +++++----
 pom.xml                                       |  6 ++---
 44 files changed, 270 insertions(+), 255 deletions(-)

diff --git a/MetFragLib/pom.xml b/MetFragLib/pom.xml
index 36da6b03..23c4197c 100644
--- a/MetFragLib/pom.xml
+++ b/MetFragLib/pom.xml
@@ -43,8 +43,8 @@
 			<artifactId>postgresql</artifactId>
 		</dependency>
 		<dependency>
-			<groupId>mysql</groupId>
-			<artifactId>mysql-connector-java</artifactId>
+			<groupId>com.mysql</groupId>
+			<artifactId>mysql-connector-j</artifactId>
 		</dependency>
 		<dependency>
 			<groupId>net.sourceforge.jexcelapi</groupId>
diff --git a/MetFragRest/pom.xml b/MetFragRest/pom.xml
index 89e078fc..b51f9671 100644
--- a/MetFragRest/pom.xml
+++ b/MetFragRest/pom.xml
@@ -44,15 +44,20 @@
 	<groupId>org.springframework.boot</groupId>
 	<artifactId>spring-boot-starter-hateoas</artifactId>
 </dependency>
-
-<!--		<dependency>
-			<groupId>org.apache.logging.log4j</groupId>
-			<artifactId>log4j-api</artifactId>
-		</dependency>
 		<dependency>
-			<groupId>org.apache.logging.log4j</groupId>
-			<artifactId>log4j-core</artifactId>
-		</dependency>-->
+			<groupId>jakarta.platform</groupId>
+			<artifactId>jakarta.jakartaee-api</artifactId>
+			<scope>compile</scope>
+		</dependency>
+
+		<!--		<dependency>
+                    <groupId>org.apache.logging.log4j</groupId>
+                    <artifactId>log4j-api</artifactId>
+                </dependency>
+                <dependency>
+                    <groupId>org.apache.logging.log4j</groupId>
+                    <artifactId>log4j-core</artifactId>
+                </dependency>-->
 	</dependencies>
 	<dependencyManagement>
 		<dependencies>
diff --git a/MetFragRest/src/main/java/de/ipbhalle/metfragrest/MetFragRestController.java b/MetFragRest/src/main/java/de/ipbhalle/metfragrest/MetFragRestController.java
index 33be1b0c..28100977 100644
--- a/MetFragRest/src/main/java/de/ipbhalle/metfragrest/MetFragRestController.java
+++ b/MetFragRest/src/main/java/de/ipbhalle/metfragrest/MetFragRestController.java
@@ -13,7 +13,7 @@
 import java.util.zip.ZipEntry;
 import java.util.zip.ZipOutputStream;
 
-import javax.servlet.http.HttpServletResponse;
+import jakarta.servlet.http.HttpServletResponse;
 
 import org.apache.log4j.Logger;
 import org.apache.tomcat.util.http.fileupload.FileUtils;
diff --git a/MetFragWeb/src/main/java/de/ipbhalle/metfragweb/controller/MetFragWebBean.java b/MetFragWeb/src/main/java/de/ipbhalle/metfragweb/controller/MetFragWebBean.java
index be4628f9..f5664e0d 100644
--- a/MetFragWeb/src/main/java/de/ipbhalle/metfragweb/controller/MetFragWebBean.java
+++ b/MetFragWeb/src/main/java/de/ipbhalle/metfragweb/controller/MetFragWebBean.java
@@ -232,7 +232,6 @@ private void generateFolders() {
 		catch(Exception e) {
 			e.printStackTrace();
 			System.err.println("error generating session folders");
-			return;
 		}
 	}
 	
@@ -339,7 +338,6 @@ else if(!PositiveDoubleValueValidator.check(this.beanSettingsContainer.getMeasur
 		} catch(Exception e) {
 			e.printStackTrace();
 			this.errorMessages.setMessage("inputMeasuredMassError", "Error: Error calculating mass value.");
-			return;
 		}
 	}
 	
@@ -3157,7 +3155,7 @@ public void submitFeedbackListener(ActionEvent actionEvent) {
 			FileStorer fileStorer = new FileStorer();
 			try {
 				StreamedContent zipContent = this.beanSettingsContainer.getUserOutputDataHandler().getDownloadParameters(this.errorMessages, null);
-				zipFileToAttach = fileStorer.saveUploadedFile(zipContent.getStream(), feedbackFolder.getAbsoluteFile(), "MetFragWeb_Parameters.zip");
+				zipFileToAttach = fileStorer.saveUploadedFile(zipContent.getStream().get(), feedbackFolder.getAbsoluteFile(), "MetFragWeb_Parameters.zip");
 				addMsg += "Zip: yes" + ls;
 			}
 			catch(Exception e) {
@@ -3242,7 +3240,7 @@ public void submitFeedbackListener(ActionEvent actionEvent) {
 	}
 	
 	public String getServerName() {
-        String hostname = "";
+        String hostname;
         try {
                 hostname = InetAddress.getLocalHost().getHostName();
         } catch (UnknownHostException e) {
diff --git a/MetFragWeb/src/main/webapp/WEB-INF/faces-config.xml b/MetFragWeb/src/main/webapp/WEB-INF/faces-config.xml
index 7418148a..1729888d 100644
--- a/MetFragWeb/src/main/webapp/WEB-INF/faces-config.xml
+++ b/MetFragWeb/src/main/webapp/WEB-INF/faces-config.xml
@@ -1,9 +1,8 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<faces-config
-    xmlns="http://xmlns.jcp.org/xml/ns/javaee"
-    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-    xsi:schemaLocation="http://xmlns.jcp.org/xml/ns/javaee http://xmlns.jcp.org/xml/ns/javaee/web-facesconfig_2_2.xsd"
-    version="2.2">
+<?xml version="1.0" encoding='UTF-8'?>
+<faces-config version="3.0" xmlns="https://jakarta.ee/xml/ns/jakartaee"
+			  xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+			  xsi:schemaLocation="https://jakarta.ee/xml/ns/jakartaee
+              https://jakarta.ee/xml/ns/jakartaee/web-facesconfig_3_0.xsd">
 	<managed-bean>
 		<managed-bean-name>metFragBean</managed-bean-name>
 		<managed-bean-class>de.ipbhalle.metfragweb.controller.MetFragWebBean</managed-bean-class>
diff --git a/MetFragWeb/src/main/webapp/WEB-INF/web.xml b/MetFragWeb/src/main/webapp/WEB-INF/web.xml
index a8030641..77947b24 100644
--- a/MetFragWeb/src/main/webapp/WEB-INF/web.xml
+++ b/MetFragWeb/src/main/webapp/WEB-INF/web.xml
@@ -1,9 +1,8 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<web-app xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-	xmlns="http://java.sun.com/xml/ns/javaee"
-	xmlns:web="http://java.sun.com/xml/ns/javaee/web-app_2_5.xsd"
-	xsi:schemaLocation="http://java.sun.com/xml/ns/javaee http://java.sun.com/xml/ns/javaee/web-app_3_0.xsd"
-	id="WebApp_ID" version="3.0">
+<web-app xmlns="https://jakarta.ee/xml/ns/jakartaee"
+		 xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+		 xsi:schemaLocation="https://jakarta.ee/xml/ns/jakartaee https://jakarta.ee/xml/ns/jakartaee/web-app_5_0.xsd"
+		 version="5.0">
 	<display-name>MetFragWeb</display-name>
 	<welcome-file-list>
 		<welcome-file>index.xhtml</welcome-file>
diff --git a/MetFragWeb/src/main/webapp/comparespectrad3js.xhtml b/MetFragWeb/src/main/webapp/comparespectrad3js.xhtml
index 312f5cc4..bd62939c 100644
--- a/MetFragWeb/src/main/webapp/comparespectrad3js.xhtml
+++ b/MetFragWeb/src/main/webapp/comparespectrad3js.xhtml
@@ -1,12 +1,12 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" 
-          "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+		"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 <html xmlns="http://www.w3.org/1999/xhtml"
-	xmlns:ui="http://java.sun.com/jsf/facelets"
-	xmlns:h="http://java.sun.com/jsf/html">
+	  xmlns:ui="http://xmlns.jcp.org/jsf/facelets"
+	  xmlns:h="http://xmlns.jcp.org/jsf/html">
 <h:head>
 	<title><ui:insert name="title">MetFrag</ui:insert></title>
-	<h:outputStylesheet type='text/css'
-		name='https://fonts.googleapis.com/css?family=Lato:300,400' />
+	<link rel="stylesheet" href="https://fonts.googleapis.com/css2?family=Lato:wght@300;400&amp;display=swap" />
 	<h:outputStylesheet name='css/style.css' rel='stylesheet'
 		type='text/css' />
 	<h:outputStylesheet name='css/d3js.css' rel='stylesheet'
diff --git a/MetFragWeb/src/main/webapp/includes/candiateScoreDistribution.xhtml b/MetFragWeb/src/main/webapp/includes/candiateScoreDistribution.xhtml
index 70ec86ad..76460db5 100644
--- a/MetFragWeb/src/main/webapp/includes/candiateScoreDistribution.xhtml
+++ b/MetFragWeb/src/main/webapp/includes/candiateScoreDistribution.xhtml
@@ -1,15 +1,16 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" 
-          "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+		"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 <html xmlns="http://www.w3.org/1999/xhtml"
-	xmlns:h="http://java.sun.com/jsf/html"
-	xmlns:ui="http://java.sun.com/jsf/facelets">
+	  xmlns:ui="http://xmlns.jcp.org/jsf/facelets"
+	  xmlns:h="http://xmlns.jcp.org/jsf/html">
 
 <h:body>
 
 	<ui:composition xmlns="http://www.w3.org/1999/xhtml"
-		xmlns:h="http://java.sun.com/jsf/html"
-		xmlns:f="http://java.sun.com/jsf/core"
-		xmlns:c="http://java.sun.com/jsp/jstl/core"
+		xmlns:h="http://xmlns.jcp.org/jsf/html"
+		xmlns:f="http://xmlns.jcp.org/jsf/core"
+		xmlns:c="http://xmlns.jcp.org/jsp/jstl/core"
 		xmlns:p="http://primefaces.org/ui">
 		<h:panelGrid style="width: 100%;" columns="1"
 			rendered="#{metFragWebBean.scoreDistributionModelAvailable}">
diff --git a/MetFragWeb/src/main/webapp/includes/candidateFiltersPrime.xhtml b/MetFragWeb/src/main/webapp/includes/candidateFiltersPrime.xhtml
index e761a280..90b9ab94 100644
--- a/MetFragWeb/src/main/webapp/includes/candidateFiltersPrime.xhtml
+++ b/MetFragWeb/src/main/webapp/includes/candidateFiltersPrime.xhtml
@@ -1,13 +1,14 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" 
-          "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+		"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 <html xmlns="http://www.w3.org/1999/xhtml"
-	xmlns:h="http://java.sun.com/jsf/html"
-	xmlns:ui="http://java.sun.com/jsf/facelets">
+	  xmlns:ui="http://xmlns.jcp.org/jsf/facelets"
+	  xmlns:h="http://xmlns.jcp.org/jsf/html">
 
 <h:body>
 	<ui:composition xmlns="http://www.w3.org/1999/xhtml"
-		xmlns:h="http://java.sun.com/jsf/html"
-		xmlns:f="http://java.sun.com/jsf/core"
+		xmlns:h="http://xmlns.jcp.org/jsf/html"
+		xmlns:f="http://xmlns.jcp.org/jsf/core"
 		xmlns:p="http://primefaces.org/ui">
 
 		<h:panelGroup id="filterSettingsPanel"
diff --git a/MetFragWeb/src/main/webapp/includes/candidateFiltersScoresPrime.xhtml b/MetFragWeb/src/main/webapp/includes/candidateFiltersScoresPrime.xhtml
index 59a435d8..0ff980d9 100644
--- a/MetFragWeb/src/main/webapp/includes/candidateFiltersScoresPrime.xhtml
+++ b/MetFragWeb/src/main/webapp/includes/candidateFiltersScoresPrime.xhtml
@@ -1,13 +1,14 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" 
-          "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+		"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 <html xmlns="http://www.w3.org/1999/xhtml"
-	xmlns:h="http://java.sun.com/jsf/html"
-	xmlns:ui="http://java.sun.com/jsf/facelets">
+	  xmlns:ui="http://xmlns.jcp.org/jsf/facelets"
+	  xmlns:h="http://xmlns.jcp.org/jsf/html">
 
 <h:body>
 	<ui:composition xmlns="http://www.w3.org/1999/xhtml"
-		xmlns:h="http://java.sun.com/jsf/html"
-		xmlns:f="http://java.sun.com/jsf/core"
+		xmlns:h="http://xmlns.jcp.org/jsf/html"
+		xmlns:f="http://xmlns.jcp.org/jsf/core"
 		xmlns:p="http://primefaces.org/ui">
 		<div class="ui-grid">
 			<div class="ui-grid-row">
diff --git a/MetFragWeb/src/main/webapp/includes/candidateScoresPrime.xhtml b/MetFragWeb/src/main/webapp/includes/candidateScoresPrime.xhtml
index c8435866..8d546db6 100644
--- a/MetFragWeb/src/main/webapp/includes/candidateScoresPrime.xhtml
+++ b/MetFragWeb/src/main/webapp/includes/candidateScoresPrime.xhtml
@@ -1,14 +1,15 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" 
-          "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+		"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 <html xmlns="http://www.w3.org/1999/xhtml"
-	xmlns:h="http://java.sun.com/jsf/html"
-	xmlns:ui="http://java.sun.com/jsf/facelets">
+	  xmlns:ui="http://xmlns.jcp.org/jsf/facelets"
+	  xmlns:h="http://xmlns.jcp.org/jsf/html">
 
 <h:body>
 	<ui:composition xmlns="http://www.w3.org/1999/xhtml"
-		xmlns:h="http://java.sun.com/jsf/html"
-		xmlns:f="http://java.sun.com/jsf/core"
-		xmlns:c="http://java.sun.com/jsp/jstl/core"
+		xmlns:h="http://xmlns.jcp.org/jsf/html"
+		xmlns:f="http://xmlns.jcp.org/jsf/core"
+		xmlns:c="http://xmlns.jcp.org/jsp/jstl/core"
 		xmlns:p="http://primefaces.org/ui">
 		<h:panelGroup id="scoreSettingsPanel"
 			rendered="#{metFragWebBean.numberCompoundsRetrieved > 0}">
diff --git a/MetFragWeb/src/main/webapp/includes/comparespectraD3JSInclude.xhtml b/MetFragWeb/src/main/webapp/includes/comparespectraD3JSInclude.xhtml
index 49767624..c069949d 100644
--- a/MetFragWeb/src/main/webapp/includes/comparespectraD3JSInclude.xhtml
+++ b/MetFragWeb/src/main/webapp/includes/comparespectraD3JSInclude.xhtml
@@ -1,15 +1,16 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" 
-          "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+		"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 <html xmlns="http://www.w3.org/1999/xhtml"
-	xmlns:h="http://java.sun.com/jsf/html"
-	xmlns:ui="http://java.sun.com/jsf/facelets">
+	  xmlns:ui="http://xmlns.jcp.org/jsf/facelets"
+	  xmlns:h="http://xmlns.jcp.org/jsf/html">
 
 <h:body>
 
 	<ui:composition xmlns="http://www.w3.org/1999/xhtml"
-		xmlns:h="http://java.sun.com/jsf/html"
-		xmlns:f="http://java.sun.com/jsf/core"
-		xmlns:c="http://java.sun.com/jsp/jstl/core"
+		xmlns:h="http://xmlns.jcp.org/jsf/html"
+		xmlns:f="http://xmlns.jcp.org/jsf/core"
+		xmlns:c="http://xmlns.jcp.org/jsp/jstl/core"
 		xmlns:p="http://primefaces.org/ui" xmlns:pe="http://primefaces.org/ui">
 		<script type="text/javascript" src="https://d3js.org/d3.v3.min.js"></script>
 		<script type="text/javascript"
diff --git a/MetFragWeb/src/main/webapp/includes/databasePrime.xhtml b/MetFragWeb/src/main/webapp/includes/databasePrime.xhtml
index f144ad6d..8ec52803 100644
--- a/MetFragWeb/src/main/webapp/includes/databasePrime.xhtml
+++ b/MetFragWeb/src/main/webapp/includes/databasePrime.xhtml
@@ -1,15 +1,16 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" 
-          "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+		"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 <html xmlns="http://www.w3.org/1999/xhtml"
-	xmlns:h="http://java.sun.com/jsf/html"
-	xmlns:ui="http://java.sun.com/jsf/facelets">
+	  xmlns:ui="http://xmlns.jcp.org/jsf/facelets"
+	  xmlns:h="http://xmlns.jcp.org/jsf/html">
 
 <h:body>
 
 	<ui:composition xmlns="http://www.w3.org/1999/xhtml"
-		xmlns:h="http://java.sun.com/jsf/html"
-		xmlns:f="http://java.sun.com/jsf/core"
-		xmlns:c="http://java.sun.com/jsp/jstl/core"
+		xmlns:h="http://xmlns.jcp.org/jsf/html"
+		xmlns:f="http://xmlns.jcp.org/jsf/core"
+		xmlns:c="http://xmlns.jcp.org/jsp/jstl/core"
 		xmlns:p="http://primefaces.org/ui">
 		<div class="ui-grid">
 			<div class="ui-grid-row">
diff --git a/MetFragWeb/src/main/webapp/includes/dialogs/aboutDialog.xhtml b/MetFragWeb/src/main/webapp/includes/dialogs/aboutDialog.xhtml
index de39df9c..214c5fa2 100644
--- a/MetFragWeb/src/main/webapp/includes/dialogs/aboutDialog.xhtml
+++ b/MetFragWeb/src/main/webapp/includes/dialogs/aboutDialog.xhtml
@@ -1,10 +1,11 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" 
-          "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+		"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 <html xmlns="http://www.w3.org/1999/xhtml"
-	xmlns:ui="http://java.sun.com/jsf/facelets"
-	xmlns:h="http://java.sun.com/jsf/html"
-	xmlns:p="http://primefaces.org/ui"
-	xmlns:f="http://java.sun.com/jsf/core">
+	  xmlns:ui="http://xmlns.jcp.org/jsf/facelets"
+	  xmlns:h="http://xmlns.jcp.org/jsf/html"
+	  xmlns:f="http://xmlns.jcp.org/jsf/core"
+	  xmlns:p="http://primefaces.org/ui">
 
 <h:body>
 	<h:form id="aboutDialogForm">
diff --git a/MetFragWeb/src/main/webapp/includes/dialogs/downloadCandidatesDialog.xhtml b/MetFragWeb/src/main/webapp/includes/dialogs/downloadCandidatesDialog.xhtml
index 4eb4f552..c371f297 100644
--- a/MetFragWeb/src/main/webapp/includes/dialogs/downloadCandidatesDialog.xhtml
+++ b/MetFragWeb/src/main/webapp/includes/dialogs/downloadCandidatesDialog.xhtml
@@ -1,9 +1,10 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" 
-          "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+		"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 <html xmlns="http://www.w3.org/1999/xhtml"
-	xmlns:ui="http://java.sun.com/jsf/facelets"
-	xmlns:h="http://java.sun.com/jsf/html"
-	xmlns:p="http://primefaces.org/ui">
+	  xmlns:ui="http://xmlns.jcp.org/jsf/facelets"
+	  xmlns:h="http://xmlns.jcp.org/jsf/html"
+	  xmlns:p="http://primefaces.org/ui">
 
 <h:body>
 	<p:dialog id="downloadCandidatesDialog" header="Select format" widgetVar="downloadCandidatesDialog"
diff --git a/MetFragWeb/src/main/webapp/includes/dialogs/downloadParametersDialog.xhtml b/MetFragWeb/src/main/webapp/includes/dialogs/downloadParametersDialog.xhtml
index 82731a88..b3f0e430 100644
--- a/MetFragWeb/src/main/webapp/includes/dialogs/downloadParametersDialog.xhtml
+++ b/MetFragWeb/src/main/webapp/includes/dialogs/downloadParametersDialog.xhtml
@@ -1,9 +1,10 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" 
-          "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+		"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 <html xmlns="http://www.w3.org/1999/xhtml"
-	xmlns:ui="http://java.sun.com/jsf/facelets"
-	xmlns:h="http://java.sun.com/jsf/html"
-	xmlns:p="http://primefaces.org/ui">
+	  xmlns:ui="http://xmlns.jcp.org/jsf/facelets"
+	  xmlns:h="http://xmlns.jcp.org/jsf/html"
+	  xmlns:p="http://primefaces.org/ui">
 
 <h:body>
 	<ui:composition>
diff --git a/MetFragWeb/src/main/webapp/includes/dialogs/downloadResultsDialog.xhtml b/MetFragWeb/src/main/webapp/includes/dialogs/downloadResultsDialog.xhtml
index 42e76512..ce40c96d 100644
--- a/MetFragWeb/src/main/webapp/includes/dialogs/downloadResultsDialog.xhtml
+++ b/MetFragWeb/src/main/webapp/includes/dialogs/downloadResultsDialog.xhtml
@@ -1,9 +1,10 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" 
-          "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+		"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 <html xmlns="http://www.w3.org/1999/xhtml"
-	xmlns:ui="http://java.sun.com/jsf/facelets"
-	xmlns:h="http://java.sun.com/jsf/html"
-	xmlns:p="http://primefaces.org/ui">
+	  xmlns:ui="http://xmlns.jcp.org/jsf/facelets"
+	  xmlns:h="http://xmlns.jcp.org/jsf/html"
+	  xmlns:p="http://primefaces.org/ui">
 
 <h:body>
 	<p:dialog id="downloadResultsDialog" header="Select format" widgetVar="downloadResultsDialog"
diff --git a/MetFragWeb/src/main/webapp/includes/dialogs/expiredSessionDialog.xhtml b/MetFragWeb/src/main/webapp/includes/dialogs/expiredSessionDialog.xhtml
index 59a37f21..b994aaa5 100644
--- a/MetFragWeb/src/main/webapp/includes/dialogs/expiredSessionDialog.xhtml
+++ b/MetFragWeb/src/main/webapp/includes/dialogs/expiredSessionDialog.xhtml
@@ -1,9 +1,10 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" 
-          "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+		"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 <html xmlns="http://www.w3.org/1999/xhtml"
-	xmlns:ui="http://java.sun.com/jsf/facelets"
-	xmlns:h="http://java.sun.com/jsf/html"
-	xmlns:p="http://primefaces.org/ui">
+	  xmlns:ui="http://xmlns.jcp.org/jsf/facelets"
+	  xmlns:h="http://xmlns.jcp.org/jsf/html"
+	  xmlns:p="http://primefaces.org/ui">
 
 <h:body>
 
diff --git a/MetFragWeb/src/main/webapp/includes/dialogs/feedbackButtonDialog.xhtml b/MetFragWeb/src/main/webapp/includes/dialogs/feedbackButtonDialog.xhtml
index 5fa4e7de..5e05ebca 100644
--- a/MetFragWeb/src/main/webapp/includes/dialogs/feedbackButtonDialog.xhtml
+++ b/MetFragWeb/src/main/webapp/includes/dialogs/feedbackButtonDialog.xhtml
@@ -1,10 +1,11 @@
+<?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
-          "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+		"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 <html xmlns="http://www.w3.org/1999/xhtml"
-	xmlns:ui="http://java.sun.com/jsf/facelets"
-	xmlns:h="http://java.sun.com/jsf/html"
-	xmlns:p="http://primefaces.org/ui"
-	xmlns:f="http://java.sun.com/jsf/core">
+	  xmlns:ui="http://xmlns.jcp.org/jsf/facelets"
+	  xmlns:h="http://xmlns.jcp.org/jsf/html"
+	  xmlns:p="http://primefaces.org/ui"
+	  xmlns:f="http://xmlns.jcp.org/jsf/core">
 
 <h:body>
 	<h:panelGroup styleClass="feedback" layout="block">
diff --git a/MetFragWeb/src/main/webapp/includes/dialogs/feedbackDialog.xhtml b/MetFragWeb/src/main/webapp/includes/dialogs/feedbackDialog.xhtml
index 62e74a1c..f8b92e29 100644
--- a/MetFragWeb/src/main/webapp/includes/dialogs/feedbackDialog.xhtml
+++ b/MetFragWeb/src/main/webapp/includes/dialogs/feedbackDialog.xhtml
@@ -1,10 +1,10 @@
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" 
           "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 <html xmlns="http://www.w3.org/1999/xhtml"
-	xmlns:ui="http://java.sun.com/jsf/facelets"
-	xmlns:h="http://java.sun.com/jsf/html"
+	xmlns:ui="http://xmlns.jcp.org/jsf/facelets"
+	xmlns:h="http://xmlns.jcp.org/jsf/html"
 	xmlns:p="http://primefaces.org/ui"
-	xmlns:f="http://java.sun.com/jsf/core">
+	xmlns:f="http://xmlns.jcp.org/jsf/core">
 
 <h:body>
 	<h:form id="feedbackDialogForm">
diff --git a/MetFragWeb/src/main/webapp/includes/dialogs/fragmentsViewDialog.xhtml b/MetFragWeb/src/main/webapp/includes/dialogs/fragmentsViewDialog.xhtml
index d09a1d84..c99d34ed 100644
--- a/MetFragWeb/src/main/webapp/includes/dialogs/fragmentsViewDialog.xhtml
+++ b/MetFragWeb/src/main/webapp/includes/dialogs/fragmentsViewDialog.xhtml
@@ -1,10 +1,11 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" 
-          "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+		"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 <html xmlns="http://www.w3.org/1999/xhtml"
-	xmlns:ui="http://java.sun.com/jsf/facelets"
-	xmlns:h="http://java.sun.com/jsf/html"
-	xmlns:p="http://primefaces.org/ui"
-	xmlns:f="http://java.sun.com/jsf/core">
+	  xmlns:ui="http://xmlns.jcp.org/jsf/facelets"
+	  xmlns:h="http://xmlns.jcp.org/jsf/html"
+	  xmlns:p="http://primefaces.org/ui"
+	  xmlns:f="http://xmlns.jcp.org/jsf/core">
 
 <h:body>
 	<h:outputScript library="primefaces" name="jquery/jquery.js"
diff --git a/MetFragWeb/src/main/webapp/includes/dialogs/processCandidatesProgressDialog.xhtml b/MetFragWeb/src/main/webapp/includes/dialogs/processCandidatesProgressDialog.xhtml
index f2265d11..b053ba20 100644
--- a/MetFragWeb/src/main/webapp/includes/dialogs/processCandidatesProgressDialog.xhtml
+++ b/MetFragWeb/src/main/webapp/includes/dialogs/processCandidatesProgressDialog.xhtml
@@ -1,9 +1,10 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" 
-          "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+		"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 <html xmlns="http://www.w3.org/1999/xhtml"
-	xmlns:ui="http://java.sun.com/jsf/facelets"
-	xmlns:h="http://java.sun.com/jsf/html"
-	xmlns:p="http://primefaces.org/ui">
+	  xmlns:ui="http://xmlns.jcp.org/jsf/facelets"
+	  xmlns:h="http://xmlns.jcp.org/jsf/html"
+	  xmlns:p="http://primefaces.org/ui">
 
 <h:body>
 
diff --git a/MetFragWeb/src/main/webapp/includes/dialogs/retrieveCandidatesProgressDialog.xhtml b/MetFragWeb/src/main/webapp/includes/dialogs/retrieveCandidatesProgressDialog.xhtml
index a407b432..1282f4d6 100644
--- a/MetFragWeb/src/main/webapp/includes/dialogs/retrieveCandidatesProgressDialog.xhtml
+++ b/MetFragWeb/src/main/webapp/includes/dialogs/retrieveCandidatesProgressDialog.xhtml
@@ -1,9 +1,10 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" 
-          "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+		"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 <html xmlns="http://www.w3.org/1999/xhtml"
-	xmlns:ui="http://java.sun.com/jsf/facelets"
-	xmlns:h="http://java.sun.com/jsf/html"
-	xmlns:p="http://primefaces.org/ui">
+	  xmlns:ui="http://xmlns.jcp.org/jsf/facelets"
+	  xmlns:h="http://xmlns.jcp.org/jsf/html"
+	  xmlns:p="http://primefaces.org/ui">
 
 <h:body>
 
diff --git a/MetFragWeb/src/main/webapp/includes/dialogs/scoresViewDialog.xhtml b/MetFragWeb/src/main/webapp/includes/dialogs/scoresViewDialog.xhtml
index d8de4c6c..382f3c1a 100644
--- a/MetFragWeb/src/main/webapp/includes/dialogs/scoresViewDialog.xhtml
+++ b/MetFragWeb/src/main/webapp/includes/dialogs/scoresViewDialog.xhtml
@@ -1,10 +1,11 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" 
-          "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+		"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 <html xmlns="http://www.w3.org/1999/xhtml"
-	xmlns:ui="http://java.sun.com/jsf/facelets"
-	xmlns:h="http://java.sun.com/jsf/html"
-	xmlns:p="http://primefaces.org/ui"
-	xmlns:f="http://java.sun.com/jsf/core">
+	  xmlns:ui="http://xmlns.jcp.org/jsf/facelets"
+	  xmlns:h="http://xmlns.jcp.org/jsf/html"
+	  xmlns:p="http://primefaces.org/ui"
+	  xmlns:f="http://xmlns.jcp.org/jsf/core">
 
 <h:body>
 	<p:dialog width="655" dynamic="true" visible="#{metFragWebBean.scoresViewActive}"
diff --git a/MetFragWeb/src/main/webapp/includes/dialogs/spectrumViewDialog.xhtml b/MetFragWeb/src/main/webapp/includes/dialogs/spectrumViewDialog.xhtml
index 984e0702..f4715e50 100644
--- a/MetFragWeb/src/main/webapp/includes/dialogs/spectrumViewDialog.xhtml
+++ b/MetFragWeb/src/main/webapp/includes/dialogs/spectrumViewDialog.xhtml
@@ -1,9 +1,10 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" 
-          "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+		"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 <html xmlns="http://www.w3.org/1999/xhtml"
-	xmlns:ui="http://java.sun.com/jsf/facelets"
-	xmlns:h="http://java.sun.com/jsf/html"
-	xmlns:p="http://primefaces.org/ui">
+	  xmlns:ui="http://xmlns.jcp.org/jsf/facelets"
+	  xmlns:h="http://xmlns.jcp.org/jsf/html"
+	  xmlns:p="http://primefaces.org/ui">
 
 <h:body>
 	<p:dialog visible="#{metFragWebBean.spectrumViewActive}" id="spectrumViewDialog" header="Spectrum View" widgetVar="spectrumViewDialog"
diff --git a/MetFragWeb/src/main/webapp/includes/errorpages/viewExpired.xhtml b/MetFragWeb/src/main/webapp/includes/errorpages/viewExpired.xhtml
index e4779cee..9419532a 100644
--- a/MetFragWeb/src/main/webapp/includes/errorpages/viewExpired.xhtml
+++ b/MetFragWeb/src/main/webapp/includes/errorpages/viewExpired.xhtml
@@ -1,7 +1,12 @@
-
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+        "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 <html xmlns="http://www.w3.org/1999/xhtml"
-     xmlns:h="http://java.sun.com/jsf/html"
-     xmlns:f="http://java.sun.com/jsf/core">
+      xmlns:ui="http://xmlns.jcp.org/jsf/facelets"
+      xmlns:h="http://xmlns.jcp.org/jsf/html"
+      xmlns:p="http://primefaces.org/ui"
+      xmlns:f="http://xmlns.jcp.org/jsf/core">
+
   <title>Nice View Expired Page</title>
 </h:head>
  
diff --git a/MetFragWeb/src/main/webapp/includes/footer.xhtml b/MetFragWeb/src/main/webapp/includes/footer.xhtml
index bea02400..f418ef0e 100644
--- a/MetFragWeb/src/main/webapp/includes/footer.xhtml
+++ b/MetFragWeb/src/main/webapp/includes/footer.xhtml
@@ -1,8 +1,9 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" 
-          "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+		"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 <html xmlns="http://www.w3.org/1999/xhtml"
-	xmlns:ui="http://java.sun.com/jsf/facelets"
-	xmlns:h="http://java.sun.com/jsf/html">
+	  xmlns:ui="http://xmlns.jcp.org/jsf/facelets"
+	  xmlns:h="http://xmlns.jcp.org/jsf/html">
 
 <h:body>
 	<ui:composition>
diff --git a/MetFragWeb/src/main/webapp/includes/fragmentationPrime.xhtml b/MetFragWeb/src/main/webapp/includes/fragmentationPrime.xhtml
index ffa90763..c083331c 100644
--- a/MetFragWeb/src/main/webapp/includes/fragmentationPrime.xhtml
+++ b/MetFragWeb/src/main/webapp/includes/fragmentationPrime.xhtml
@@ -1,16 +1,17 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" 
-          "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+		"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 <html xmlns="http://www.w3.org/1999/xhtml"
-	xmlns:h="http://java.sun.com/jsf/html"
-	xmlns:ui="http://java.sun.com/jsf/facelets">
+	  xmlns:ui="http://xmlns.jcp.org/jsf/facelets"
+	  xmlns:h="http://xmlns.jcp.org/jsf/html">
 
 <h:body>
 
 
 	<ui:composition xmlns="http://www.w3.org/1999/xhtml"
-		xmlns:h="http://java.sun.com/jsf/html"
-		xmlns:f="http://java.sun.com/jsf/core"
-		xmlns:c="http://java.sun.com/jsp/jstl/core"
+		xmlns:h="http://xmlns.jcp.org/jsf/html"
+		xmlns:f="http://xmlns.jcp.org/jsf/core"
+		xmlns:c="http://xmlns.jcp.org/jsp/jstl/core"
 		xmlns:p="http://primefaces.org/ui" xmlns:pe="http://primefaces.org/ui">
 
 		<div class="ui-grid">
diff --git a/MetFragWeb/src/main/webapp/includes/header.xhtml b/MetFragWeb/src/main/webapp/includes/header.xhtml
index e5fdd7a4..78e29675 100644
--- a/MetFragWeb/src/main/webapp/includes/header.xhtml
+++ b/MetFragWeb/src/main/webapp/includes/header.xhtml
@@ -1,8 +1,9 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" 
-          "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+		"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 <html xmlns="http://www.w3.org/1999/xhtml"
-      xmlns:ui="http://java.sun.com/jsf/facelets"
-      xmlns:h="http://java.sun.com/jsf/html">
+	  xmlns:ui="http://xmlns.jcp.org/jsf/facelets"
+	  xmlns:h="http://xmlns.jcp.org/jsf/html">
 
 <h:body>
 		<ui:composition>
diff --git a/MetFragWeb/src/main/webapp/includes/landingPage.xhtml b/MetFragWeb/src/main/webapp/includes/landingPage.xhtml
index de30e8c9..196da1af 100644
--- a/MetFragWeb/src/main/webapp/includes/landingPage.xhtml
+++ b/MetFragWeb/src/main/webapp/includes/landingPage.xhtml
@@ -1,14 +1,15 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" 
-          "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+		"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 <html xmlns="http://www.w3.org/1999/xhtml"
-	xmlns:h="http://java.sun.com/jsf/html"
-	xmlns:ui="http://java.sun.com/jsf/facelets">
+	  xmlns:ui="http://xmlns.jcp.org/jsf/facelets"
+	  xmlns:h="http://xmlns.jcp.org/jsf/html">
 
 <h:body>
 	<ui:composition xmlns="http://www.w3.org/1999/xhtml"
-		xmlns:h="http://java.sun.com/jsf/html"
-		xmlns:f="http://java.sun.com/jsf/core"
-		xmlns:c="http://java.sun.com/jsp/jstl/core"
+		xmlns:h="http://xmlns.jcp.org/jsf/html"
+		xmlns:f="http://xmlns.jcp.org/jsf/core"
+		xmlns:c="http://xmlns.jcp.org/jsp/jstl/core"
 		xmlns:p="http://primefaces.org/ui">
 
 		<h:form id="landingPageForm" enctype="multipart/form-data">
diff --git a/MetFragWeb/src/main/webapp/includes/main.xhtml b/MetFragWeb/src/main/webapp/includes/main.xhtml
index 10674659..b4752e77 100644
--- a/MetFragWeb/src/main/webapp/includes/main.xhtml
+++ b/MetFragWeb/src/main/webapp/includes/main.xhtml
@@ -1,15 +1,16 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" 
-          "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+		"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 <html xmlns="http://www.w3.org/1999/xhtml"
-	xmlns:h="http://java.sun.com/jsf/html"
-	xmlns:ui="http://java.sun.com/jsf/facelets">
+	  xmlns:ui="http://xmlns.jcp.org/jsf/facelets"
+	  xmlns:h="http://xmlns.jcp.org/jsf/html">
 
 <h:body>
 	
 	<ui:composition xmlns="http://www.w3.org/1999/xhtml"
-		xmlns:h="http://java.sun.com/jsf/html"
-		xmlns:f="http://java.sun.com/jsf/core"
-		xmlns:c="http://java.sun.com/jsp/jstl/core"
+		xmlns:h="http://xmlns.jcp.org/jsf/html"
+		xmlns:f="http://xmlns.jcp.org/jsf/core"
+		xmlns:c="http://xmlns.jcp.org/jsp/jstl/core"
 		xmlns:p="http://primefaces.org/ui">
 		
 		<h:form id="mainForm" enctype="multipart/form-data">
diff --git a/MetFragWeb/src/main/webapp/includes/resultCluster.xhtml b/MetFragWeb/src/main/webapp/includes/resultCluster.xhtml
index 457351ae..e4962f58 100644
--- a/MetFragWeb/src/main/webapp/includes/resultCluster.xhtml
+++ b/MetFragWeb/src/main/webapp/includes/resultCluster.xhtml
@@ -1,15 +1,16 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" 
-          "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+		"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 <html xmlns="http://www.w3.org/1999/xhtml"
-	xmlns:h="http://java.sun.com/jsf/html"
-	xmlns:ui="http://java.sun.com/jsf/facelets">
+	  xmlns:ui="http://xmlns.jcp.org/jsf/facelets"
+	  xmlns:h="http://xmlns.jcp.org/jsf/html">
 
 <h:body>
 
 	<ui:composition xmlns="http://www.w3.org/1999/xhtml"
-		xmlns:h="http://java.sun.com/jsf/html"
-		xmlns:f="http://java.sun.com/jsf/core"
-		xmlns:c="http://java.sun.com/jsp/jstl/core"
+		xmlns:h="http://xmlns.jcp.org/jsf/html"
+		xmlns:f="http://xmlns.jcp.org/jsf/core"
+		xmlns:c="http://xmlns.jcp.org/jsp/jstl/core"
 		xmlns:p="http://primefaces.org/ui">
 
 		<style>
diff --git a/MetFragWeb/src/main/webapp/includes/resultTable.xhtml b/MetFragWeb/src/main/webapp/includes/resultTable.xhtml
index af314939..bf12d04b 100644
--- a/MetFragWeb/src/main/webapp/includes/resultTable.xhtml
+++ b/MetFragWeb/src/main/webapp/includes/resultTable.xhtml
@@ -1,15 +1,16 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" 
-          "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+		"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 <html xmlns="http://www.w3.org/1999/xhtml"
-	xmlns:h="http://java.sun.com/jsf/html"
-	xmlns:ui="http://java.sun.com/jsf/facelets">
+	  xmlns:ui="http://xmlns.jcp.org/jsf/facelets"
+	  xmlns:h="http://xmlns.jcp.org/jsf/html">
 
 <h:body>
 
 	<ui:composition xmlns="http://www.w3.org/1999/xhtml"
-		xmlns:h="http://java.sun.com/jsf/html"
-		xmlns:f="http://java.sun.com/jsf/core"
-		xmlns:c="http://java.sun.com/jsp/jstl/core"
+		xmlns:h="http://xmlns.jcp.org/jsf/html"
+		xmlns:f="http://xmlns.jcp.org/jsf/core"
+		xmlns:c="http://xmlns.jcp.org/jsp/jstl/core"
 		xmlns:p="http://primefaces.org/ui">
 		<h:panelGroup id="resultsTablePanel"
 			rendered="#{metFragWebBean.resultsAvailable}">
diff --git a/MetFragWeb/src/main/webapp/includes/statistics.xhtml b/MetFragWeb/src/main/webapp/includes/statistics.xhtml
index 632005fe..5b43164a 100644
--- a/MetFragWeb/src/main/webapp/includes/statistics.xhtml
+++ b/MetFragWeb/src/main/webapp/includes/statistics.xhtml
@@ -1,15 +1,16 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" 
-          "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+		"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 <html xmlns="http://www.w3.org/1999/xhtml"
-	xmlns:h="http://java.sun.com/jsf/html"
-	xmlns:ui="http://java.sun.com/jsf/facelets">
+	  xmlns:ui="http://xmlns.jcp.org/jsf/facelets"
+	  xmlns:h="http://xmlns.jcp.org/jsf/html">
 
 <h:body>
 
 	<ui:composition xmlns="http://www.w3.org/1999/xhtml"
-		xmlns:h="http://java.sun.com/jsf/html"
-		xmlns:f="http://java.sun.com/jsf/core"
-		xmlns:c="http://java.sun.com/jsp/jstl/core"
+		xmlns:h="http://xmlns.jcp.org/jsf/html"
+		xmlns:f="http://xmlns.jcp.org/jsf/core"
+		xmlns:c="http://xmlns.jcp.org/jsp/jstl/core"
 		xmlns:p="http://primefaces.org/ui">
 		<h:panelGroup id="statisticsPanel"
 			rendered="#{metFragWebBean.scoreDistributionModelAvailable}">
diff --git a/MetFragWeb/src/main/webapp/includes/tooltips/databasePrimeTooltips.xhtml b/MetFragWeb/src/main/webapp/includes/tooltips/databasePrimeTooltips.xhtml
index 1f344f96..c474d120 100644
--- a/MetFragWeb/src/main/webapp/includes/tooltips/databasePrimeTooltips.xhtml
+++ b/MetFragWeb/src/main/webapp/includes/tooltips/databasePrimeTooltips.xhtml
@@ -1,9 +1,10 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" 
-          "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+		"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 <html xmlns="http://www.w3.org/1999/xhtml"
-	xmlns:ui="http://java.sun.com/jsf/facelets"
-	xmlns:h="http://java.sun.com/jsf/html"
-	xmlns:p="http://primefaces.org/ui">
+	  xmlns:ui="http://xmlns.jcp.org/jsf/facelets"
+	  xmlns:h="http://xmlns.jcp.org/jsf/html"
+	  xmlns:p="http://primefaces.org/ui">
 
 <h:body>
 	<!--  -->
diff --git a/MetFragWeb/src/main/webapp/includes/tooltips/filterPrimeTooltips.xhtml b/MetFragWeb/src/main/webapp/includes/tooltips/filterPrimeTooltips.xhtml
index 58799a4d..8cb7af0d 100644
--- a/MetFragWeb/src/main/webapp/includes/tooltips/filterPrimeTooltips.xhtml
+++ b/MetFragWeb/src/main/webapp/includes/tooltips/filterPrimeTooltips.xhtml
@@ -1,9 +1,10 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" 
-          "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+		"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 <html xmlns="http://www.w3.org/1999/xhtml"
-	xmlns:ui="http://java.sun.com/jsf/facelets"
-	xmlns:h="http://java.sun.com/jsf/html"
-	xmlns:p="http://primefaces.org/ui">
+	  xmlns:ui="http://xmlns.jcp.org/jsf/facelets"
+	  xmlns:h="http://xmlns.jcp.org/jsf/html"
+	  xmlns:p="http://primefaces.org/ui">
 
 <h:body>
 	<!--  -->
diff --git a/MetFragWeb/src/main/webapp/includes/tooltips/fragmentationPrimeTooltips.xhtml b/MetFragWeb/src/main/webapp/includes/tooltips/fragmentationPrimeTooltips.xhtml
index 15fcce79..2a14be94 100644
--- a/MetFragWeb/src/main/webapp/includes/tooltips/fragmentationPrimeTooltips.xhtml
+++ b/MetFragWeb/src/main/webapp/includes/tooltips/fragmentationPrimeTooltips.xhtml
@@ -1,9 +1,10 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" 
-          "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+		"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 <html xmlns="http://www.w3.org/1999/xhtml"
-	xmlns:ui="http://java.sun.com/jsf/facelets"
-	xmlns:h="http://java.sun.com/jsf/html"
-	xmlns:p="http://primefaces.org/ui">
+	  xmlns:ui="http://xmlns.jcp.org/jsf/facelets"
+	  xmlns:h="http://xmlns.jcp.org/jsf/html"
+	  xmlns:p="http://primefaces.org/ui">
 
 <h:body>
 	<!--  -->
diff --git a/MetFragWeb/src/main/webapp/includes/tooltips/scorePrimeTooltips.xhtml b/MetFragWeb/src/main/webapp/includes/tooltips/scorePrimeTooltips.xhtml
index 749f6871..48cf6fc4 100644
--- a/MetFragWeb/src/main/webapp/includes/tooltips/scorePrimeTooltips.xhtml
+++ b/MetFragWeb/src/main/webapp/includes/tooltips/scorePrimeTooltips.xhtml
@@ -1,9 +1,10 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" 
-          "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+		"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 <html xmlns="http://www.w3.org/1999/xhtml"
-	xmlns:ui="http://java.sun.com/jsf/facelets"
-	xmlns:h="http://java.sun.com/jsf/html"
-	xmlns:p="http://primefaces.org/ui">
+	  xmlns:ui="http://xmlns.jcp.org/jsf/facelets"
+	  xmlns:h="http://xmlns.jcp.org/jsf/html"
+	  xmlns:p="http://primefaces.org/ui">
 
 <h:body>
 	<p:tooltip styleClass="tooltip" escape="false" id="smartsInclusionScoreLabelTooltip" for="smartsInclusionScoreLabel" >
diff --git a/MetFragWeb/src/main/webapp/includes/uploadParameters.xhtml b/MetFragWeb/src/main/webapp/includes/uploadParameters.xhtml
index ee5f939b..20280e2b 100644
--- a/MetFragWeb/src/main/webapp/includes/uploadParameters.xhtml
+++ b/MetFragWeb/src/main/webapp/includes/uploadParameters.xhtml
@@ -1,15 +1,16 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" 
-          "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+		"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 <html xmlns="http://www.w3.org/1999/xhtml"
-	xmlns:h="http://java.sun.com/jsf/html"
-	xmlns:ui="http://java.sun.com/jsf/facelets">
+	  xmlns:ui="http://xmlns.jcp.org/jsf/facelets"
+	  xmlns:h="http://xmlns.jcp.org/jsf/html">
 
 <h:body>
 
 	<ui:composition xmlns="http://www.w3.org/1999/xhtml"
-		xmlns:h="http://java.sun.com/jsf/html"
-		xmlns:f="http://java.sun.com/jsf/core"
-		xmlns:c="http://java.sun.com/jsp/jstl/core"
+		xmlns:h="http://xmlns.jcp.org/jsf/html"
+		xmlns:f="http://xmlns.jcp.org/jsf/core"
+		xmlns:c="http://xmlns.jcp.org/jsp/jstl/core"
 		xmlns:p="http://primefaces.org/ui">
 
 		<h:form id="uploadParametersForm" enctype="multipart/form-data">
diff --git a/MetFragWeb/src/main/webapp/index.xhtml b/MetFragWeb/src/main/webapp/index.xhtml
index 1beb40a7..81065502 100644
--- a/MetFragWeb/src/main/webapp/index.xhtml
+++ b/MetFragWeb/src/main/webapp/index.xhtml
@@ -1,11 +1,12 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" 
-          "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+		"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 <html xmlns="http://www.w3.org/1999/xhtml"
-	xmlns:ui="http://java.sun.com/jsf/facelets"
-	xmlns:h="http://java.sun.com/jsf/html">
+	  xmlns:ui="http://xmlns.jcp.org/jsf/facelets"
+	  xmlns:h="http://xmlns.jcp.org/jsf/html">
 <h:head>
 	<title><ui:insert name="title">MetFrag</ui:insert></title>
-	<h:outputStylesheet type='text/css' name='https://fonts.googleapis.com/css?family=Lato:300,400' />
+	<link rel="stylesheet" href="https://fonts.googleapis.com/css2?family=Lato:wght@300;400&amp;display=swap" />
 	<h:outputStylesheet name='css/style.css'  rel='stylesheet' type='text/css'/>
 	<meta name="viewport" content="width=device-width" />
 </h:head>
diff --git a/MetFragWeb/src/main/webapp/landing.xhtml b/MetFragWeb/src/main/webapp/landing.xhtml
index a3c3116d..81a090b5 100644
--- a/MetFragWeb/src/main/webapp/landing.xhtml
+++ b/MetFragWeb/src/main/webapp/landing.xhtml
@@ -1,11 +1,12 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" 
-          "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+		"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 <html xmlns="http://www.w3.org/1999/xhtml"
-	xmlns:ui="http://java.sun.com/jsf/facelets"
-	xmlns:h="http://java.sun.com/jsf/html">
+	  xmlns:ui="http://xmlns.jcp.org/jsf/facelets"
+	  xmlns:h="http://xmlns.jcp.org/jsf/html">
 <h:head>
 	<title><ui:insert name="title">MetFrag</ui:insert></title>
-	<h:outputStylesheet type='text/css' name='https://fonts.googleapis.com/css?family=Lato:300,400' />
+	<link rel="stylesheet" href="https://fonts.googleapis.com/css2?family=Lato:wght@300;400&amp;display=swap" />
 	<h:outputStylesheet name='css/style.css'  rel='stylesheet' type='text/css'/>
 </h:head>
 
diff --git a/MetFragWeb/src/main/webapp/resources/css/style.css b/MetFragWeb/src/main/webapp/resources/css/style.css
index 60554ba4..23ea7ec0 100644
--- a/MetFragWeb/src/main/webapp/resources/css/style.css
+++ b/MetFragWeb/src/main/webapp/resources/css/style.css
@@ -313,14 +313,6 @@ html,body {
 .ui-messages-error-icon-user {
 	height: 24px;
 	width: 24px;
-	/*
-	background: transparent
-		url("/MetFragWeb/javax.faces.resource/messages/messages.png.xhtml?ln=primefaces&v=4_0_0_141104&v=5.3")
-		no-repeat scroll 0% 0%;
-	background-color: transparent;
-	background-image:
-		url("/MetFragWeb/javax.faces.resource/messages/messages.png.xhtml?ln=primefaces&v=4_0_0_141104&v=5.3");
-	*/
 	background-image: url("#{resource['images/icons/messages.png']}");
 	background-color: transparent;
 	background-repeat: no-repeat;
@@ -360,14 +352,6 @@ html,body {
 .ui-messages-info-icon-user {
 	height: 24px;
 	width: 24px;
-	/*
-	background: transparent
-		url("/MetFragWeb/javax.faces.resource/messages/messages.png.xhtml?ln=primefaces&v=4_0_0_141104&v=5.3")
-		no-repeat scroll 0% 0%;
-	background-color: transparent;
-	background-image:
-		url("/MetFragWeb/javax.faces.resource/messages/messages.png.xhtml?ln=primefaces&v=4_0_0_141104&v=5.3");
-	*/
 	background-image: url("#{resource['images/icons/messages.png']}");
 	background-color: transparent;
 	background-repeat: no-repeat;
@@ -407,14 +391,6 @@ html,body {
 .ui-messages-warning-icon-user {
 	height: 24px;
 	width: 24px;
-	/*
-	background: transparent
-		url("/MetFragWeb/javax.faces.resource/messages/messages.png.xhtml?ln=primefaces&v=4_0_0_141104&v=5.3")
-		no-repeat scroll 0% 0%;
-	background-color: transparent;
-	background-image:
-		url("/MetFragWeb/javax.faces.resource/messages/messages.png.xhtml?ln=primefaces&v=4_0_0_141104&v=5.3");
-	*/
 	background-image: url("#{resource['images/icons/messages.png']}");
 	background-color: transparent;
 	background-repeat: no-repeat;
diff --git a/MetFragWeb/src/main/webapp/upload.xhtml b/MetFragWeb/src/main/webapp/upload.xhtml
index 7616a944..c1936318 100644
--- a/MetFragWeb/src/main/webapp/upload.xhtml
+++ b/MetFragWeb/src/main/webapp/upload.xhtml
@@ -1,11 +1,12 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" 
-          "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+		"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 <html xmlns="http://www.w3.org/1999/xhtml"
-	xmlns:ui="http://java.sun.com/jsf/facelets"
-	xmlns:h="http://java.sun.com/jsf/html">
+	  xmlns:ui="http://xmlns.jcp.org/jsf/facelets"
+	  xmlns:h="http://xmlns.jcp.org/jsf/html">
 <h:head>
 	<title><ui:insert name="title">MetFrag</ui:insert></title>
-	<h:outputStylesheet type='text/css' name='https://fonts.googleapis.com/css?family=Lato:300,400' />
+	<link rel="stylesheet" href="https://fonts.googleapis.com/css2?family=Lato:wght@300;400&amp;display=swap" />
 	<h:outputStylesheet name='css/style.css'  rel='stylesheet' type='text/css'/>
 </h:head>
 
diff --git a/pom.xml b/pom.xml
index 3812674f..9c0cc4ef 100644
--- a/pom.xml
+++ b/pom.xml
@@ -63,8 +63,8 @@
 				<version>42.7.4</version>
 			</dependency>
 			<dependency>
-				<groupId>mysql</groupId>
-				<artifactId>mysql-connector-java</artifactId>
+				<groupId>com.mysql</groupId>
+				<artifactId>mysql-connector-j</artifactId>
 				<version>8.0.33</version>
 			</dependency>
 			<dependency>
@@ -128,7 +128,7 @@
 			<dependency>
 				<groupId>org.primefaces</groupId>
 				<artifactId>primefaces</artifactId>
-				<version>10.0.0</version>
+				<version>12.0.0</version>
 				<classifier>jakarta</classifier>
 			</dependency>
 			<dependency>